Aliphatic Ether Bond Formation Expands the Scope of Radical SAM Enzymes in Natural Product Biosynthesis

2019 ◽  
Vol 141 (27) ◽  
pp. 10610-10615 ◽  
Author(s):  
Kenzie A. Clark ◽  
Leah B. Bushin ◽  
Mohammad R. Seyedsayamdost
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Radical Sam ◽  
Natural Product Biosynthesis ◽  
Radical Sam Enzymes ◽  
Ether Bond ◽  
Aliphatic Ether

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

2021 ◽  
Author(s):  
Sofie Dekimpe ◽  
Joleen Masschelein
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Peptide Bond ◽  
Chemical Diversity ◽  
Peptide Bond Formation ◽  
Natural Product Biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.

scholarly journals Thioether bond formation by SPASM domain radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis

2016 ◽  
Vol 52 (37) ◽  
pp. 6249-6252 ◽  
Author(s):  
Alhosna Benjdia ◽  
Alain Guillot ◽  
Benjamin Lefranc ◽  
Hubert Vaudry ◽  
Jérôme Leprince ◽  
...  
Keyword(s):  
Bond Formation ◽  
Radical Sam ◽  
Radical Sam Enzymes ◽  
Radical Sam Enzyme ◽  
Synthetic Approaches

The radical SAM enzyme AlbA has been reported to catalyze the formation of a thioether bond in the antibiotic subtilosin A. By modeling, biochemical and synthetic approaches, we propose novel mechanistic perspectives on this emerging group of enzymes.

scholarly journals Heteroatom–Heteroatom Bond Formation in Natural Product Biosynthesis

2017 ◽  
Vol 117 (8) ◽  
pp. 5784-5863 ◽  
Author(s):  
Abraham J. Waldman ◽  
Tai L. Ng ◽  
Peng Wang ◽  
Emily P. Balskus
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Natural Product Biosynthesis

scholarly journals 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis

MedChemComm ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 1517-1530 ◽  
Author(s):  
Risa Nofiani ◽  
Benjamin Philmus ◽  
Yosi Nindita ◽  
Taifo Mahmud
Keyword(s):  
Natural Product ◽  
Significant Role ◽  
Bond Formation ◽  
Natural Product Biosynthesis

KAS III-like enzymes play a significant role in natural product biosynthesis through C–C, C–O, and/or C–N bond formation.

scholarly journals Accumulation of an unprecedented 5′-deoxyadenos-4′-yl radical unmasks the kinetics of the radical-mediated C-C bond formation step in MoaA catalysis

2020 ◽  
Author(s):  
Haoran Pang ◽  
Edward A. Lilla ◽  
Pan Zhang ◽  
Du Zhang ◽  
Thomas P. Shields ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
Bond Formation ◽  
Kinetic Characterization ◽  
Amino Acid Residues ◽  
Radical Sam ◽  
Radical Sam Enzymes ◽  
Rate Acceleration ◽  
Radical Sam Enzyme ◽  
Radical Catalysis

AbstractRadical S-adenosyl-L-methionine (SAM) enzymes catalyze various free radical-mediated reactions. In these enzymes, the rate-determining SAM cleavage kinetically masks all the subsequent steps. Due to this kinetic masking, detailed mechanistic characterization of radical transformations catalyzed by these enzymes is very difficult. Here, we report a successful kinetic characterization of the radical C-C bond formation catalyzed by a MoaA radical SAM enzyme. MoaA catalyzes an unprecedented 3′,8-cyclization of GTP into 3′,8-cyclo-7,8-dihydro-GTP (3′,8-cH2GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterization, we found that MoaA accumulates a 5′-deoxyadenos-4′-yl radical (5′-dA-C4′•) under the turnover conditions, and forms (4′S)-5′-deoxyadenosine ((4′S)-5′-dA), which is a C-4′ epimer of the naturally occurring (4′R)-5′-dA. Together with kinetic characterizations, these observations revealed the presence of a shunt pathway in which an on-pathway intermediate, GTP C-3′ radical, abstracts H-4′ atom from 5′-dA to transiently generate 5′-dA-C4′• that is subsequently reduced stereospecifically to yield (4′S)-5′-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics, and determined the rate of the on-pathway 3′,8-cyclization step as 2.7 ± 0.7 s−1. Together with DFT calculations, this observation suggested that the 3′,8-cyclization is accelerated by 6 ∼ 9 orders of magnitude by MoaA. Potential contributions of the active-site amino acid residues, and their potential relationships with human Moco deficiency disease are discussed. This is the first determination of the magnitude of catalytic rate acceleration by a radical SAM enzyme, and provides the foundation for understanding how radical SAM enzymes achieve highly specific radical catalysis.

scholarly journals Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes

2020 ◽  
Vol 295 (49) ◽  
pp. 16665-16677
Author(s):  
Clémence Balty ◽  
Alain Guillot ◽  
Laura Fradale ◽  
Clémence Brewee ◽  
Benjamin Lefranc ◽  
...  
Keyword(s):  
Bond Formation ◽  
Large Family ◽  
Leader Peptide ◽  
Human Pathogens ◽  
Metabolic Potential ◽  
Radical Sam ◽  
Radical Sam Enzymes ◽  
Peptide Recognition ◽  
Recognition Element ◽  
Data Support

Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether–containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC–MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.

scholarly journals C–C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products

2018 ◽  
Vol 35 (7) ◽  
pp. 660-694 ◽  
Author(s):  
Kenichi Yokoyama ◽  
Edward A. Lilla
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Radical Sam ◽  
Radical Sam Enzymes ◽  
Bond Forming ◽  
Cofactor Biosynthesis

An emerging group of radical SAM enzymes that catalyze C–C bond formations in natural product and cofactor biosynthesis are discussed.

scholarly journals Enzymatic Carbon–Sulfur Bond Formation in Natural Product Biosynthesis

2017 ◽  
Vol 117 (8) ◽  
pp. 5521-5577 ◽  
Author(s):  
Kyle L. Dunbar ◽  
Daniel H. Scharf ◽  
Agnieszka Litomska ◽  
Christian Hertweck
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Natural Product Biosynthesis ◽  
Sulfur Bond
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